Loading required package: S4Vectors
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb

Attaching package: 'GenomeInfoDb'

The following objects are masked from 'package:BiocGenerics':

    organism, species

Error: package or namespace load failed for 'GenomicRanges':
 Functions found when exporting methods from the namespace 'GenomicRanges' which are not S4 generic: 'queryHits', 'subjectHits'
Error: package 'GenomicRanges' could not be loaded
In addition: Warning messages:
1: multiple methods tables found for 'organism' 
2: multiple methods tables found for 'species' 
3: replacing previous import 'BiocGenerics::species' by 'GenomeInfoDb::species' when loading 'GenomicRanges' 
4: replacing previous import 'BiocGenerics::organism' by 'GenomeInfoDb::organism' when loading 'GenomicRanges' 
5: no function found corresponding to methods exports from 'GenomicRanges' for: 'compare', 'map', 'mapCoords', 'ngap', 'splitAsListReturnedClass' 
Execution halted
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'DiffExp_v2_LncRNA_Exonic_Only_Male_3h_Vehicle_Male_3h_TCPOBOP.txt': No such file or directory
Execution halted
Loading required package: grid
Loading required package: futile.logger
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'Down_Genes_DESeq_LncRNA_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt': No such file or directory
Execution halted
Loading required package: grid
Loading required package: futile.logger
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'Up_Genes_DESeq_LncRNA_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt': No such file or directory
Execution halted
cat: Count.Table.*.txt: No such file or directory
rm: cannot remove `Count.Table.*.txt': No such file or directory
mv: cannot stat `DiffExp_v2_LncRNA_Exonic_Only_Male_3h_Vehicle_Male_3h_TCPOBOP.txt': No such file or directory
cp: cannot stat `/scratch/386633.1.linga/Input/DiffExp_v2_LncRNA_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt': No such file or directory
cp: cannot stat `/scratch/386633.1.linga/Input/Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload*': No such file or directory
cp: cannot stat `/scratch/386633.1.linga/Input/*_Genes*.txt': No such file or directory
cp: cannot stat `/scratch/386633.1.linga/Input/*.png': No such file or directory
mv: cannot stat `*.png': No such file or directory